1. 12 Mar, 2020 5 commits
  2. 05 Mar, 2020 1 commit
  3. 28 Feb, 2020 1 commit
  4. 25 Feb, 2020 1 commit
  5. 24 Feb, 2020 4 commits
  6. 21 Feb, 2020 2 commits
    • Overduin, Sam's avatar
      Delete aa_todo_notes · 04a75dfc
      Overduin, Sam authored
      04a75dfc
    • Overduin, Sam's avatar
      Impl. taxaSPAdes as option with --taxonomy as argument & some clean-up · ae290f75
      Overduin, Sam authored
      
      
      config.info:
      - Added taxonomy false.
      
      barcode_index_builder.hpp:
      - only extract TaxaTree if cfg::get().taxonomy
      
      scaffold_graph_construction_pipeline.cpp:
      - only add TaxaBreak constructor if cfg::get().taxonomy
      
      config_struct.cpp & hpp:
      - added taxonomy to cfg.
      
      barcode_index_construction.cpp:
      - Only decide LCA if cfg::get().taxonomy
      
      spades_iteration_stage.py:
      - Add taxonomy option to config.info of final iteration
      
      options_parser.py:
      - Add --taxonomy argument. Only usable with --meta and --gemcode options.
      
      Some various other clean-ups in files:
      - aa_todo_notes
      - path_polisher.hpp
      - path_scaffolder.cpp
      - scaffold_vertex.cpp
      Signed-off-by: Overduin, Sam's avatarOverduin, Sam <sam.overduin@wur.nl>
      ae290f75
  7. 06 Feb, 2020 1 commit
    • Overduin, Sam's avatar
      Impl. LCA for PathVertex::GetTaxaTree, TaxaBreak during scaffolding. · a3d9211c
      Overduin, Sam authored
      
      
      scaffold_vertex.hpp & cpp:
      - Used Fuzzy LCA for PathVertex::GetTaxaTree with max_drilldown_ratio=0.4,
        max_mismatch_ratio=0.03 and min_assignment_ratio=0.3. This code is in
        barcode_index_construction.cpp
      
      barcode_index.hpp & barcode_index_builder.hpp:
      - added code to deal with "_SUBSTR(0,106)" at end of read names (influenced
       taxatrees).
      
      launcher.cpp:
      - Removed LCA parameter testing to start of repeat resolving step
      
      read_cloud_connection_conditions.cpp & hpp:
      - Output which edge connections (or path connections) are being broken in
        logfile.
      
      scaffold_graph_construction_pipeline.cpp:
      - Moved TaxaBreakConstructor to bottom of pipelines for more informative
        breaks.
      
      path_scaffolder.cpp:
      - map.at() replaced with map[] if item not within map. Added debuggin msg.
      
      barcode_index_construction.cpp:
      - Added function to get LCA for PathScaffoldVertex (more conservative than
        reads-> contig LCA).
      - Started prototype code for taxonomy assignment per edges (eg. using CAT)
      Signed-off-by: Overduin, Sam's avatarOverduin, Sam <sam.overduin@wur.nl>
      a3d9211c
  8. 15 Jan, 2020 1 commit
    • Overduin, Sam's avatar
      Impl. PathVertex::GetTaxaTree, enabled LCA testing & moved TaxaBreak forwards · 74d6406f
      Overduin, Sam authored
      
      
      scaffold_vertex.hpp & cpp:
      - Made GetTaxaTree() member of PathVertex and EdgeIdVertex (both are
        ScaffoldVertexes in the contracted DeBruijnGraph)
      
      launcher.cpp:
      - Added LCA parameter testing to start of repeat resolving step
      
      read_cloud_connection_conditions.cpp & hpp:
      - Made GetTaxaTree() part of the ScaffoldVertex itself (Edge- & Path-type)
      
      scaffold_graph_construction_pipeline.cpp:
      - Moved TaxaBreakConstructor to top of pipelines for efficiency
      
      barcode_index_construction.cpp:
      - Turned LCA settings tester back on
      
      barcode_index_construction.cpp & hpp:
      - Re-implemented taxonomy assignment with fuzzy_lca
      - Some cleaner code in taxonomy assignment
      - Added parameter testing module
      - Bugfixes, header file updated
      
      read_cloud_connection_conditions.cpp & hpp:
      - Code cleanup (remove duplicated logic)
      
      construction_callers & scaffold_graph_construction_pipeline:
      - Nothing (just code that was commented out again)
      Signed-off-by: Overduin, Sam's avatarOverduin, Sam <sam.overduin@wur.nl>
      74d6406f
  9. 08 Jan, 2020 1 commit
    • Overduin, Sam's avatar
      Impl. final contig taxa assignment (fuzzy_lca), parameter testing module & fixes · cb555c2d
      Overduin, Sam authored
      
      
      barcode_index.hpp:
      - Improved robustness of some functions (error handling)
      - Added taxid_distribution serialisation
      
      barcode_index_construction.cpp & hpp:
      - Re-implemented taxonomy assignment with fuzzy_lca
      - Some cleaner code in taxonomy assignment
      - Added parameter testing module
      - Bugfixes, header file updated
      
      read_cloud_connection_conditions.cpp & hpp:
      - Code cleanup (remove duplicated logic)
      
      construction_callers & scaffold_graph_construction_pipeline:
      - Nothing (just code that was commented out again)
      Signed-off-by: Overduin, Sam's avatarOverduin, Sam <sam.overduin@wur.nl>
      cb555c2d
  10. 06 Dec, 2019 1 commit
    • Overduin, Sam's avatar
      Impl. extra BarcodeIndex serialisation, use conjugate edges & edges to fasta output · c8303759
      Overduin, Sam authored
      barcode_index.hpp:
      - Implemented taxa_codes + taxonomy_ serialisation
      - Made taxa_codes::map's public
      
      barcode_info_extractor.hpp:
      - Added funcs: EdgeIsValid, GetConjugateEdge, GetSequence, GetEdgeLength
      
      barcode_index_construction.cpp:
      - Added write_contigs_to_fasta for testing purposes.
      - Re-implemented taxonomy assignment to use edge & conjugate.
      
      read_cloud_connection_conditions.cpp:
      - In TaxaBreakPred.: if taxonomy of edge not found, try taxonomy of
        conjugate edge. Else taxa 0.
      
      logger.hpp:
      - Created special DEBUG_SAM for personal logging. Will change at end.
      c8303759
  11. 03 Dec, 2019 1 commit
    • Overduin, Sam's avatar
      Improved taxonomy assignment & implemented taxonomy transition filter. · 5b1631c0
      Overduin, Sam authored
      barcode_index.hpp:
      - Initialized TaxIdEncoder with "0" taxatree
      - Added func TaxIdEncoder::ToTaxaTreeVector
      - Bugfix EdgeEntry::GetTaxonomy()
      
      barcode_info_extractor.hpp:
      - Added funcs: ToTaxaTreeVector, TaxaTreeFromTaxId, GetTaxaTreeFromEdge
      
      barcode_index_construction.cpp:
      - Moved ToTaxaTreeVector to extractor & barcode_index
      - Improved majority_vote_lca to actually use LCA
      
      construction_callers.cpp & hpp:
      - Added TaxaBreakConstructorCaller to break mismatched taxa in
        contracted assembly graph
      
      read_cloud_connection_conditions.cpp:
      - Added TaxaBreakPredicate that returns false when transition
        (scaffold_edge) has incompatible taxonomy
      
      scaffold_graph_construction_pipeline.cpp:
      - Added TaxaBreak routine to basic mode & scaffolding mode
      5b1631c0
  12. 29 Nov, 2019 1 commit
    • Overduin, Sam's avatar
      barcode_index_builder.hpp: · ba6cfe86
      Overduin, Sam authored
      - Added no TaxaTree in read means taxa '0'
      - Bugfix taxatree_prefixes
      - Cut out taxatree parser to vector<int>
      
      barcode_index.hpp:
      - Changed TaxIdEncoder to fully use TaxId vs int64
      - small bugfixes eg: moved declarations around, corrected taxid_begin()
      - made edge_to_entry in FrameBarcodeIndex public
      
      barcode_info_extractor.hpp:
      - Added GetTaxidCount
      
      barcode_index_construction.cpp:
      - Added chunk of code to determine and set LCA per EdgeEntry in barcode_index
      ba6cfe86
  13. 27 Nov, 2019 1 commit
    • Overduin, Sam's avatar
      barcode_index_builder.hpp: · d471de51
      Overduin, Sam authored
      - Added TaxaTree (like 1.23.456.7890) parser from reads & store in index
      
      barcode_index.hpp:
      - Added data structure in BarcodeIndex to store TaxaTree mapping
        to taxids (taxatree_codes_).
      - Added data structure in EdgeEntry to store taxid_distribution_.
      - Added attribute to EdgeEntry for taxonomy_.
      
      barcode_info_extractor.hpp:
      - Added method to get taxids for a EdgeID
      d471de51
  14. 22 Nov, 2019 1 commit
  15. 18 Nov, 2019 1 commit